Newer generations of Allied fighters caught up in speed, and eventually, the Ki-48 was too slow to outrun them, while superior modern Japanese aircraft, such as the Yokosuka P1Y and the Mitsubishi Ki-67, could only be produced in small numbers.

The aircraft served in China from June 1940, replacing the Kawasaki Ki-32, and were widely used in the Philippines, Malaya, Burma, New Guinea, the Solomon Islands and the Dutch East Indies, where the Ki-48 Ia and Ib models, slow and badly armed, were supplemented by the marginally improved Ki-48 IIa and IIc, which were maintained in service along with the older types until the end of the war.

All models continued in service until the Battle of Okinawa during April 1945, when many were converted into kamikaze aircraft (Ki-48-II KAI Tai-Atari) armed with an 800 kg (1,760 lb) bomb.

This was due to the use of small ship formations (three to ten aircraft) escorted by large numbers of fighters (25–75), typically Nakajima Ki-43s.

On 29 January, seven Kawasaki Ki-48 of the Army's Shichisi Mitate Tokubetsu Kōgeki Tai counter-attacked the Allied fleet at low level as the British aircraft were returning from Palembang.

The British radar picture was confused by the presence of over 100 friendly aircraft, and the first two or three Supermarine Seafire CAP interceptions did not occur until just before the Ki-48 formation entered the air defence zone.

The last pair of Seafires chased the five remaining Ki-48s inside the screen and, with the support of returning Vought F4U Corsairs and Grumman F6F Hellcats which had just been scrambled, shot down all of them, amongst intense AA fire.